/*! Set the cell grid dimension.
Only allowed when file is opened in write mode.
\param mfile (CMMFile *)
\param grid (const int *) the cell grid dimension (X,Y,Z) */
void ccp4_cmap_set_grid(CMMFile *mfile, const int *grid)
{
if (ccp4_file_is_write(mfile->stream)) {
mfile->cell_grid[0] = grid[0];
mfile->cell_grid[1] = grid[1];
mfile->cell_grid[2] = grid[2];
}
}
/*! Set the stored map origin (rows,sections,columns)
Only allowed when file is opened in write mode.
\param mfile (CMMFile *)
\param origin (const int *) the origin */
void ccp4_cmap_set_origin(CMMFile *mfile, const int *origin)
{
if (ccp4_file_is_write(mfile->stream)) {
mfile->origin[0] = origin[0];
mfile->origin[1] = origin[1];
mfile->origin[2] = origin[2];
}
}
/*! Set the local header size (in bytes)
\param mfile (CMMFile *)
\param size (size_t) header size associated with each section (in bytes) */
void ccp4_cmap_set_local_header(CMMFile *mfile, size_t size)
{
if (ccp4_file_is_write(mfile->stream) && mfile->data.number == 0) {
mfile->data.header_size = size;
mfile->data.block_size = mfile->data.section_size + mfile->data.header_size;
}
return;
}
/*! Set the stored map axes order (rows,sections,columns)
where 1=X, 2=Y, 3=Z.
Only allowed when file is opened in write mode.
\param mfile (CMMFile *)
\param axes_order (const float *) the axes ordering */
void ccp4_cmap_set_order(CMMFile *mfile, const int *axes_order)
{
if (ccp4_file_is_write(mfile->stream)) {
mfile->axes_order[0] = axes_order[0];
mfile->axes_order[1] = axes_order[1];
mfile->axes_order[2] = axes_order[2];
}
}
/*! Set the map statistics, including maximum, minimum, mean and standard
deviation. This is only meaningful for datamode FLOAT32 and the file
open in write mode.
\param mfile (CMMFile *)
\param min (float)
\param max (float)
\param mean (double)
\param rms (double) */
void ccp4_cmap_set_mapstats(CMMFile *mfile, const float min, const float max,
const double mean, const double rms)
{
if (ccp4_file_is_write(mfile->stream)) {
mfile->stats.min = min;
mfile->stats.max = max;
mfile->stats.mean = mean;
mfile->stats.rms = rms;
}
}
/*! Set the cell parameters.
Only allowed when file is opened in write mode.
\param mfile (CMMFile *)
\param cell (const float *) the cell parameters */
void ccp4_cmap_set_cell(CMMFile *mfile, const float *cell)
{
if (ccp4_file_is_write(mfile->stream)) {
mfile->cell[0] = cell[0];
mfile->cell[1] = cell[1];
mfile->cell[2] = cell[2];
mfile->cell[3] = cell[3];
mfile->cell[4] = cell[4];
mfile->cell[5] = cell[5];
}
}
/*! Set the datamode.
This is only allowed if the file is opened in write mode, and
no data has been written.
\param mfile (CMMFile *)
\param datamode (unsigned int) major mode of map */
void ccp4_cmap_set_datamode(CMMFile *mfile, unsigned int datamode)
{
if (ccp4_file_is_write(mfile->stream) && !mfile->data.number &&
datamode <= 6 && datamode != 5) {
mfile->data_mode = datamode;
ccp4_file_setmode(mfile->stream, datamode);
mfile->data.section_size = mfile->map_dim[0]*mfile->map_dim[1]*
ccp4_file_itemsize(mfile->stream);
mfile->data.block_size = mfile->data.section_size +
mfile->data.header_size;
}
}
/*! Set the stored map dimension (rows,sections,columns)
Only allowed when file is opened in write mode before any data
is written.
Note: the row dimension will be overridden during writing
\param mfile (CMMFile *)
\param map_dim (const int *) the map dimension */
void ccp4_cmap_set_dim(CMMFile *mfile, const int *map_dim)
{
if (ccp4_file_is_write(mfile->stream) && !mfile->data.number) {
mfile->map_dim[0] = map_dim[0];
mfile->map_dim[1] = map_dim[1];
mfile->map_dim[2] = map_dim[2];
mfile->data.section_size = map_dim[0]*map_dim[1]*
ccp4_file_itemsize(mfile->stream);
mfile->data.block_size = mfile->data.section_size +
mfile->data.header_size;
}
}
/*! Get the map statistics, including maximum, minimum, mean and standard
deviation. This is only meaningful for datamode FLOAT32.
\param mfile (const CMMFile *)
\param min (float *)
\param max (float *)
\param mean (double *)
\param rms (double *) */
void ccp4_cmap_get_mapstats(const CMMFile *mfile, float *min, float* max,
double *mean, double *rms)
{
double f1,f2,f3;
*min = mfile->stats.min;
*max = mfile->stats.max;
if (ccp4_file_is_write(mfile->stream) && mfile->close_mode == 0) {
f1 = (mfile->stats.total != 0) ? mfile->stats.mean / mfile->stats.total : 0;
f2 = (mfile->stats.total != 0) ? mfile->stats.rms / mfile->stats.total : 0;
f3 = f2 - f1*f1;
*rms = (f3 > 0) ? sqrt(f3) : 0;
*mean = f1 - (double) mfile->stats.offset;
} else {
*mean = mfile->stats.mean;
*rms = mfile->stats.rms;
}
}
/*! Close the file.
In write mode the header is output, along with the machine
stamp. In read mode the file is just closed.
Write mode supports ways of updating the map statistics (
only active for FLOAT32).
/param mfile (CMMFile *)
/return void */
void ccp4_cmap_close(CMMFile *mfile)
{
int i;
if ( mfile == NULL)
return;
if (ccp4_file_is_write(mfile->stream) ) {
if ( mfile->data_mode == FLOAT32) {
switch (mfile->close_mode) {
case 1:
break;
case 2:
mfile->stats.offset = 0.0f;
case 0:
default:
if (mfile->stats.total != 0) {
mfile->stats.mean /= mfile->stats.total;
mfile->stats.rms /= mfile->stats.total;
mfile->stats.rms -= mfile->stats.mean*mfile->stats.mean;
mfile->stats.rms = (mfile->stats.rms > 0) ? sqrt(mfile->stats.rms) : 0;
mfile->stats.mean += (double) mfile->stats.offset;
}
break;
}
}
write_mapheader(mfile);
write_maplabels(mfile);
ccp4_file_warch(mfile->stream);
}
ccp4_file_close(mfile->stream);
for (i=0 ; i != mfile->labels.number ; i++)
if (mfile->labels.labels[i] != NULL)
free(mfile->labels.labels[i]);
free(mfile);
}
/*! Set the spacegroup listed in the map header.
Only allowed when file is opened in write mode.
\param mfile (CMMFile *)
\param spacegroup (int) spacegroup number */
void ccp4_cmap_set_spacegroup(CMMFile *mfile, int spacegroup)
{
if (ccp4_file_is_write(mfile->stream))
mfile->spacegroup = spacegroup;
}